PMC:7341831 / 705-3057
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T3 | 1268-1273 | Body_part | denotes | serum | http://purl.org/sig/ont/fma/fma63083 |
| T4 | 1676-1681 | Body_part | denotes | blood | http://purl.org/sig/ont/fma/fma9670 |
| T5 | 2038-2042 | Body_part | denotes | Lung | http://purl.org/sig/ont/fma/fma7195 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T2 | 1268-1273 | Body_part | denotes | serum | http://purl.obolibrary.org/obo/UBERON_0001977 |
| T3 | 1676-1681 | Body_part | denotes | blood | http://purl.obolibrary.org/obo/UBERON_0000178 |
| T4 | 2038-2042 | Body_part | denotes | Lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 37 | 108-116 | Species | denotes | patients | Tax:9606 |
| 38 | 192-200 | Species | denotes | Patients | Tax:9606 |
| 39 | 275-285 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 40 | 413-421 | Species | denotes | patients | Tax:9606 |
| 41 | 13-21 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 42 | 133-142 | Disease | denotes | pneumonia | MESH:D011014 |
| 43 | 147-153 | Disease | denotes | sepsis | MESH:D018805 |
| 44 | 206-241 | Disease | denotes | acute respiratory distress syndrome | MESH:D012128 |
| 45 | 249-265 | Disease | denotes | viral infections | MESH:D001102 |
| 46 | 335-348 | Disease | denotes | aspergillosis | MESH:D001228 |
| 47 | 353-375 | Disease | denotes | Invasive aspergillosis | MESH:D055744 |
| 48 | 469-488 | Disease | denotes | respiratory failure | MESH:D012131 |
| 49 | 518-527 | Disease | denotes | pneumonia | MESH:D011014 |
| 50 | 595-604 | Disease | denotes | infection | MESH:D007239 |
| 51 | 640-672 | Disease | denotes | invasive pulmonary aspergillosis | MESH:D055744 |
| 67 | 944-951 | Species | denotes | patient | Tax:9606 |
| 68 | 1160-1168 | Species | denotes | patients | Tax:9606 |
| 69 | 1227-1248 | Species | denotes | Aspergillus fumigatus | Tax:746128 |
| 70 | 1498-1506 | Species | denotes | patients | Tax:9606 |
| 71 | 1409-1420 | Species | denotes | Aspergillus | Tax:746128 |
| 72 | 859-870 | Chemical | denotes | oseltamivir | MESH:D053139 |
| 73 | 1274-1287 | Chemical | denotes | galactomannan | MESH:C012990 |
| 74 | 1289-1291 | Chemical | denotes | GM | MESH:C012990 |
| 75 | 741-750 | Disease | denotes | mortality | MESH:D003643 |
| 76 | 957-990 | Disease | denotes | severe acute respiratory syndrome | MESH:D045169 |
| 77 | 992-996 | Disease | denotes | SARS | MESH:D045169 |
| 78 | 1011-1024 | Disease | denotes | aspergillosis | MESH:D001228 |
| 79 | 1181-1189 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 80 | 1467-1480 | Disease | denotes | aspergillosis | MESH:D001228 |
| 81 | 1512-1520 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 88 | 1686-1694 | Species | denotes | patients | Tax:9606 |
| 89 | 1903-1911 | Species | denotes | patients | Tax:9606 |
| 90 | 1583-1594 | Species | denotes | Aspergillus | Tax:746128 |
| 91 | 1635-1637 | Chemical | denotes | GM | MESH:C012990 |
| 92 | 1700-1708 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 93 | 1917-1925 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 96 | 2198-2206 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 97 | 2302-2308 | Disease | denotes | deaths | MESH:D003643 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T10 | 13-21 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T11 | 67-70 | Disease | denotes | flu | http://purl.obolibrary.org/obo/MONDO_0005812 |
| T12 | 133-142 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T13 | 206-241 | Disease | denotes | acute respiratory distress syndrome | http://purl.obolibrary.org/obo/MONDO_0006502 |
| T14 | 212-241 | Disease | denotes | respiratory distress syndrome | http://purl.obolibrary.org/obo/MONDO_0009971 |
| T15 | 249-265 | Disease | denotes | viral infections | http://purl.obolibrary.org/obo/MONDO_0005108 |
| T16 | 275-283 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T17 | 275-279 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T18 | 335-348 | Disease | denotes | aspergillosis | http://purl.obolibrary.org/obo/MONDO_0005657 |
| T19 | 353-375 | Disease | denotes | Invasive aspergillosis | http://purl.obolibrary.org/obo/MONDO_0000240 |
| T20 | 362-375 | Disease | denotes | aspergillosis | http://purl.obolibrary.org/obo/MONDO_0005657 |
| T21 | 463-488 | Disease | denotes | acute respiratory failure | http://purl.obolibrary.org/obo/MONDO_0001208|http://purl.obolibrary.org/obo/MONDO_0021113 |
| T23 | 500-509 | Disease | denotes | influenza | http://purl.obolibrary.org/obo/MONDO_0005812 |
| T24 | 518-527 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T25 | 585-604 | Disease | denotes | influenza infection | http://purl.obolibrary.org/obo/MONDO_0005812 |
| T26 | 595-604 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T27 | 659-672 | Disease | denotes | aspergillosis | http://purl.obolibrary.org/obo/MONDO_0005657 |
| T28 | 692-701 | Disease | denotes | influenza | http://purl.obolibrary.org/obo/MONDO_0005812 |
| T29 | 957-990 | Disease | denotes | severe acute respiratory syndrome | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T30 | 992-996 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T31 | 1011-1024 | Disease | denotes | aspergillosis | http://purl.obolibrary.org/obo/MONDO_0005657 |
| T32 | 1181-1189 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T33 | 1467-1480 | Disease | denotes | aspergillosis | http://purl.obolibrary.org/obo/MONDO_0005657 |
| T34 | 1512-1520 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T35 | 1700-1708 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T36 | 1917-1925 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T37 | 2198-2206 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T5 | 430-431 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T6 | 532-533 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T7 | 901-902 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T8 | 942-943 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T9 | 1257-1258 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T10 | 1555-1562 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T11 | 1676-1681 | http://purl.obolibrary.org/obo/UBERON_0000178 | denotes | blood |
| T12 | 1676-1681 | http://www.ebi.ac.uk/efo/EFO_0000296 | denotes | blood |
| T13 | 1885-1886 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T14 | 2038-2042 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | Lung |
| T15 | 2038-2042 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | Lung |
| T16 | 2082-2083 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T17 | 2144-2145 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T11 | 674-677 | Chemical | denotes | IPA | http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802 |
| T13 | 713-716 | Chemical | denotes | IPA | http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802 |
| T15 | 844-849 | Chemical | denotes | drugs | http://purl.obolibrary.org/obo/CHEBI_23888 |
| T16 | 859-870 | Chemical | denotes | oseltamivir | http://purl.obolibrary.org/obo/CHEBI_7798 |
| T17 | 875-890 | Chemical | denotes | corticosteroids | http://purl.obolibrary.org/obo/CHEBI_50858 |
| T18 | 1056-1071 | Chemical | denotes | corticosteroids | http://purl.obolibrary.org/obo/CHEBI_50858 |
| T19 | 1137-1140 | Chemical | denotes | IPA | http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802 |
| T21 | 1274-1287 | Chemical | denotes | galactomannan | http://purl.obolibrary.org/obo/CHEBI_27680 |
| T22 | 1289-1291 | Chemical | denotes | GM | http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680 |
| T24 | 1293-1300 | Chemical | denotes | antigen | http://purl.obolibrary.org/obo/CHEBI_59132 |
| T25 | 1635-1637 | Chemical | denotes | GM | http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680 |
| T27 | 2084-2088 | Chemical | denotes | gold | http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1 | 249-265 | http://purl.obolibrary.org/obo/GO_0016032 | denotes | viral infections |
| T2 | 770-782 | http://purl.obolibrary.org/obo/GO_0009405 | denotes | pathogenesis |
| T3 | 1620-1630 | http://purl.obolibrary.org/obo/GO_0046903 | denotes | secretions |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T2 | 1274-1287 | GlycoEpitope | denotes | galactomannan | http://www.glycoepitope.jp/epitopes/EP0510 |
| T3 | 1289-1291 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
| T4 | 1635-1637 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T10 | 0-12 | Sentence | denotes | INTRODUCTION |
| T11 | 13-191 | Sentence | denotes | COVID-19 is characterized by asymptomatic and/or mild flu-like symptoms; however, about 20% of patients may progress to pneumonia and sepsis, thus requiring intensive support 1 . |
| T12 | 192-352 | Sentence | denotes | Patients with acute respiratory distress syndrome due to viral infections, such as SARS-CoV-2, are prone to secondary complications, including aspergillosis 2 . |
| T13 | 353-531 | Sentence | denotes | Invasive aspergillosis is not uncommon in immunocompromised patients, and is a well-described complication in acute respiratory failure and severe influenza-related pneumonia 3 . |
| T14 | 532-682 | Sentence | denotes | A retrospective multicenter cohort study showed that influenza infection was an independent risk factor for invasive pulmonary aspergillosis (IPA) 4 . |
| T15 | 683-804 | Sentence | denotes | Although influenza-associated IPA is associated with high mortality and morbidity, its pathogenesis is not well known 3 . |
| T16 | 805-917 | Sentence | denotes | Direct immunomodulation and the use of drugs, such as oseltamivir and corticosteroids, may play a role 5 , 6 . |
| T17 | 918-929 | Sentence | denotes | Wang et al. |
| T18 | 930-1072 | Sentence | denotes | 2 reported a patient with severe acute respiratory syndrome (SARS), who died of aspergillosis after prolonged treatment with corticosteroids. |
| T19 | 1073-1086 | Sentence | denotes | Blaize et al. |
| T20 | 1087-1109 | Sentence | denotes | 7 and Antinori et al. |
| T21 | 1110-1301 | Sentence | denotes | 8 reported fatal cases of IPA in immunocompetent patients with severe COVID-19, whose bronchoalveolar aspirate grew Aspergillus fumigatus and had a positive serum galactomannan (GM) antigen. |
| T22 | 1302-1317 | Sentence | denotes | Antinori et al. |
| T23 | 1318-1446 | Sentence | denotes | 8 evidenced the pathological pulmonary alterations postmortem and confirmed the infective Aspergillus via molecular techniques. |
| T24 | 1447-1543 | Sentence | denotes | It is possible that aspergillosis could predispose patients with COVID-19 to clinical worsening. |
| T25 | 1544-1864 | Sentence | denotes | Therefore, testing for the presence of Aspergillus spp in lower respiratory secretions and GM (not routinely positive in peripheral blood) in patients with COVID-19 in the intensive care unit (ICU) should be considered to allow timely treatment and avoid potential immunosuppression with the use of medications 5 , 6 . |
| T26 | 1865-2037 | Sentence | denotes | However, conducting a bronchoscopy in patients with COVID-19 is relatively contraindicated due to the biological risk and clinical deterioration caused by the procedure 9 . |
| T27 | 2038-2155 | Sentence | denotes | Lung biopsy, which might also be considered a gold standard diagnosis method, is also impractical in such a scenario. |
| T28 | 2156-2249 | Sentence | denotes | Latin America seems to be the most recent COVID-19 epicenter, after Asia, Europe, and the US. |
| T29 | 2250-2352 | Sentence | denotes | In Manaus, in the Brazilian Amazon, more than 2,000 deaths were officially reported in April/May 2020. |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T6 | 133-142 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T7 | 147-153 | Phenotype | denotes | sepsis | http://purl.obolibrary.org/obo/HP_0100806 |
| T8 | 212-232 | Phenotype | denotes | respiratory distress | http://purl.obolibrary.org/obo/HP_0002098 |
| T9 | 469-488 | Phenotype | denotes | respiratory failure | http://purl.obolibrary.org/obo/HP_0002878 |
| T10 | 518-527 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T11 | 640-672 | Phenotype | denotes | invasive pulmonary aspergillosis | http://purl.obolibrary.org/obo/HP_0020103 |
| T12 | 674-677 | Phenotype | denotes | IPA | http://purl.obolibrary.org/obo/HP_0020103 |
| T13 | 713-716 | Phenotype | denotes | IPA | http://purl.obolibrary.org/obo/HP_0020103 |
| T14 | 1137-1140 | Phenotype | denotes | IPA | http://purl.obolibrary.org/obo/HP_0020103 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32638890-12890854-134289058 | 349-350 | 12890854 | denotes | 2 |
| 32638890-30299367-134289059 | 528-529 | 30299367 | denotes | 3 |
| 32638890-30076119-134289060 | 679-680 | 30076119 | denotes | 4 |
| 32638890-30299367-134289061 | 801-802 | 30299367 | denotes | 3 |
| 32638890-29325970-134289062 | 908-909 | 29325970 | denotes | 5 |
| 32638890-12890854-134289063 | 930-931 | 12890854 | denotes | 2 |
| 32638890-32470620-134289064 | 1110-1111 | 32470620 | denotes | 8 |
| 32638890-32470620-134289065 | 1318-1319 | 32470620 | denotes | 8 |
| 32638890-29325970-134289066 | 1855-1856 | 29325970 | denotes | 5 |
LitCovid-PMC-OGER-BB
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T16 | 13-21 | SP_7 | denotes | COVID-19 |
| T17 | 212-223 | UBERON:0001004 | denotes | respiratory |
| T18 | 249-254 | NCBITaxon:10239 | denotes | viral |
| T19 | 275-285 | SP_7 | denotes | SARS-CoV-2 |
| T20 | 469-480 | UBERON:0001004 | denotes | respiratory |
| T21 | 649-658 | UBERON:0002048 | denotes | pulmonary |
| T22 | 844-849 | CHEBI:23888;CHEBI:23888 | denotes | drugs |
| T23 | 859-870 | CHEBI:7798;CHEBI:7798 | denotes | oseltamivir |
| T24 | 875-890 | CHEBI:50858;CHEBI:50858 | denotes | corticosteroids |
| T25 | 970-981 | UBERON:0001004 | denotes | respiratory |
| T26 | 992-996 | SP_10 | denotes | SARS |
| T27 | 1003-1007 | GO:0016265 | denotes | died |
| T28 | 1056-1071 | CHEBI:50858;CHEBI:50858 | denotes | corticosteroids |
| T29 | 1181-1189 | SP_7 | denotes | COVID-19 |
| T30 | 1222-1226 | GO:0040007 | denotes | grew |
| T31 | 1227-1248 | NCBITaxon:746128 | denotes | Aspergillus fumigatus |
| T32 | 1268-1273 | UBERON:0001977 | denotes | serum |
| T33 | 1274-1287 | CHEBI:27680;CHEBI:27680 | denotes | galactomannan |
| T34 | 1293-1300 | CHEBI:59132;CHEBI:59132 | denotes | antigen |
| T35 | 1348-1357 | UBERON:0002048 | denotes | pulmonary |
| T36 | 1370-1380 | GO:0016265 | denotes | postmortem |
| T37 | 1512-1520 | SP_7 | denotes | COVID-19 |
| T38 | 1583-1594 | NCBITaxon:5052 | denotes | Aspergillus |
| T39 | 1608-1619 | UBERON:0001004 | denotes | respiratory |
| T40 | 1676-1681 | UBERON:0000178 | denotes | blood |
| T41 | 1700-1708 | SP_7 | denotes | COVID-19 |
| T42 | 1726-1735 | UBERON:0007221 | denotes | care unit |
| T43 | 1917-1925 | SP_7 | denotes | COVID-19 |
| T44 | 2038-2042 | UBERON:0002048 | denotes | Lung |
| T45 | 2198-2206 | SP_7 | denotes | COVID-19 |
| T46 | 2302-2308 | GO:0016265 | denotes | deaths |
| T10975 | 13-21 | SP_7 | denotes | COVID-19 |
| T9972 | 212-223 | UBERON:0001004 | denotes | respiratory |
| T44879 | 249-254 | NCBITaxon:10239 | denotes | viral |
| T10889 | 275-285 | SP_7 | denotes | SARS-CoV-2 |
| T56159 | 469-480 | UBERON:0001004 | denotes | respiratory |
| T87696 | 649-658 | UBERON:0002048 | denotes | pulmonary |
| T74450 | 844-849 | CHEBI:23888;CHEBI:23888 | denotes | drugs |
| T70529 | 859-870 | CHEBI:7798;CHEBI:7798 | denotes | oseltamivir |
| T54454 | 875-890 | CHEBI:50858;CHEBI:50858 | denotes | corticosteroids |
| T90991 | 970-981 | UBERON:0001004 | denotes | respiratory |
| T80841 | 992-996 | SP_10 | denotes | SARS |
| T15928 | 1003-1007 | GO:0016265 | denotes | died |
| T2908 | 1056-1071 | CHEBI:50858;CHEBI:50858 | denotes | corticosteroids |
| T17935 | 1181-1189 | SP_7 | denotes | COVID-19 |
| T49431 | 1222-1226 | GO:0040007 | denotes | grew |
| T73074 | 1227-1248 | NCBITaxon:746128 | denotes | Aspergillus fumigatus |
| T55704 | 1268-1273 | UBERON:0001977 | denotes | serum |
| T61728 | 1274-1287 | CHEBI:27680;CHEBI:27680 | denotes | galactomannan |
| T66622 | 1293-1300 | CHEBI:59132;CHEBI:59132 | denotes | antigen |
| T77392 | 1348-1357 | UBERON:0002048 | denotes | pulmonary |
| T64062 | 1370-1380 | GO:0016265 | denotes | postmortem |
| T85604 | 1512-1520 | SP_7 | denotes | COVID-19 |
| T74035 | 1583-1594 | NCBITaxon:5052 | denotes | Aspergillus |
| T644 | 1608-1619 | UBERON:0001004 | denotes | respiratory |
| T47982 | 1676-1681 | UBERON:0000178 | denotes | blood |
| T97836 | 1700-1708 | SP_7 | denotes | COVID-19 |
| T31476 | 1726-1735 | UBERON:0007221 | denotes | care unit |
| T4469 | 1917-1925 | SP_7 | denotes | COVID-19 |
| T35848 | 2038-2042 | UBERON:0002048 | denotes | Lung |
| T65233 | 2198-2206 | SP_7 | denotes | COVID-19 |
| T63671 | 2302-2308 | GO:0016265 | denotes | deaths |